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From: Gorjanc G. <Gre...@bf...> - 2008-09-10 06:50:13
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... >>> 1. The working.directory is assumed to be the same directory as the >>> model.file and setting working.directory to something else doesn't help. >> >> Working directory and model.file can be in separate directories, you >> can you tell me an example where it does not work. >> > Doesn't work. See below: > > > schools.sim <- bugs (data, inits, parameters, > "/usr/local/doc/r2winbugs/schools.bug", > + n.chains=3, n.iter=1000, working.directory=".") > Warning message: > In file.create(to[okay]) : > cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason > 'Permission denied' Rodney, this is a problem with permissions and not with R2WinBUGS! /usr/local/doc folders are usually not writable for regular users. If you want to avoid this problem, you can do either: A. Put modelfile somewhere else. If there will be many users (say a whole class), you do not want that they will be overwritting the same files, do you? Putting the modelfile to a home folder of each user, makes much more sense. B. You also might change the permissions of the /usr/local/doc/r2winbugs/ folder. Actually, this is needed since the R2WinBUGS package changes some parameters related to burnin and metropolis acceptance rate in a file that resides in /usr/local/doc/r2winbugs/. I am not really aware what actually is done, since the code was written by Andrew Gelman and I just make it sure that some bits run under linux. So my recommendation is: - change permissions in /usr/local/doc/r2winbugs/ via chmod -R uga+w /usr/local/doc/r2winbugs/ - make sure that each user is using its own modelfile Regards, Gregor |
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From: Rodney S. <rsp...@mc...> - 2008-09-10 13:40:18
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Gorjanc Gregor wrote: > ... > >>>> 1. The working.directory is assumed to be the same directory as the >>>> model.file and setting working.directory to something else doesn't help. >>>> >>> Working directory and model.file can be in separate directories, you >>> can you tell me an example where it does not work. >>> >>> >> Doesn't work. See below: >> >> > schools.sim <- bugs (data, inits, parameters, >> "/usr/local/doc/r2winbugs/schools.bug", >> + n.chains=3, n.iter=1000, working.directory=".") >> Warning message: >> In file.create(to[okay]) : >> cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason >> 'Permission denied' >> > > Rodney, this is a problem with permissions and not with R2WinBUGS! /usr/local/doc folders > are usually not writable for regular users. If you want to avoid this problem, you can do either: > > A. Put modelfile somewhere else. If there will be many users (say a whole class), you do not want > that they will be overwritting the same files, do you? Putting the modelfile to a home folder of each > user, makes much more sense. > > B. You also might change the permissions of the /usr/local/doc/r2winbugs/ folder. Actually, this is needed > since the R2WinBUGS package changes some parameters related to burnin and metropolis acceptance rate in > a file that resides in /usr/local/doc/r2winbugs/. I am not really aware what actually is done, since the code > was written by Andrew Gelman and I just make it sure that some bits run under linux. > > So my recommendation is: > - change permissions in /usr/local/doc/r2winbugs/ via chmod -R uga+w /usr/local/doc/r2winbugs/ > > - make sure that each user is using its own modelfile > > Regards, Gregor > Hi Gregor: My current working directory is $HOME which is writeable. R2WinBUGS is ignoring that and using the directory of the source file. Attempting to over-ride this behavior with working-directory does not workaround the problem. Please fix. Thanks, Rodney -- Rodney Sparapani Center for Patient Care & Outcomes Research (PCOR) Sr. Biostatistician Department of Medicine Was 'Name That Tune' rigged? Medical College of Wisconsin (MCW) WWLD: What Would Lombardi Do Milwaukee, WI, USA |
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From: Gorjanc G. <Gre...@bf...> - 2008-09-10 19:47:17
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Hi Rodney, > My current working directory is $HOME which is writeable. > R2WinBUGS is ignoring that and using the directory of the source file. > Attempting to over-ride this behavior with working-directory does not > workaround the problem. Please fix. Can you please post a reproducible example so that we can check what is going on. gg |
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From: Rodney S. <rsp...@mc...> - 2008-09-10 19:58:17
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Gorjanc Gregor wrote: > > Can you please post a reproducible example so that we can check what > is going on. > > gg > > > > You will find it attached. -- Rodney Sparapani Center for Patient Care & Outcomes Research (PCOR) Sr. Biostatistician Department of Medicine Was 'Name That Tune' rigged? Medical College of Wisconsin (MCW) WWLD: What Would Lombardi Do Milwaukee, WI, USA |
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From: Uwe L. <li...@st...> - 2008-09-12 09:39:54
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I cannot reproduce on Windows even when using 3 different directories:
- one for data
- one as working directory
- one for the model file
schools <- read.table ("d:/schools.dat", header=T)
J <- nrow (schools)
y <- schools$estimate
sigma.y <- schools$sd
data <- list ("J", "y", "sigma.y")
inits <- function()
list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
sigma.theta=runif(1,0,100))
parameters <- c("theta", "mu.theta", "sigma.theta")
setwd("d:/temp")
schools.sim <- bugs (data, inits, parameters, "d:/uwe/schools.bug",
n.chains=3, n.iter=1000, working.directory="d:/temp")
Simply works for me ....
Uwe
Rodney Sparapani wrote:
> Gorjanc Gregor wrote:
>>
>> Can you please post a reproducible example so that we can check what
>> is going on.
>>
>> gg
>>
>>
>>
>>
> You will find it attached.
>
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From: Rodney S. <rsp...@mc...> - 2008-09-12 14:03:50
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Uwe Ligges wrote:
> I cannot reproduce on Windows even when using 3 different directories:
>
> - one for data
> - one as working directory
> - one for the model file
>
>
>
> schools <- read.table ("d:/schools.dat", header=T)
> J <- nrow (schools)
> y <- schools$estimate
> sigma.y <- schools$sd
> data <- list ("J", "y", "sigma.y")
> inits <- function()
> list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
> sigma.theta=runif(1,0,100))
> parameters <- c("theta", "mu.theta", "sigma.theta")
> setwd("d:/temp")
> schools.sim <- bugs (data, inits, parameters, "d:/uwe/schools.bug",
> n.chains=3, n.iter=1000, working.directory="d:/temp")
>
>
> Simply works for me ....
>
> Uwe
Hi Uwe:
But, you have the command setwd("d:/temp") and I don't. However, this does
not work around the problem either:
library(R2WinBUGS)
schools <- read.table ("/usr/local/doc/r2winbugs/schools.dat", header=T)
J <- nrow (schools)
y <- schools$estimate
sigma.y <- schools$sd
data <- list ("J", "y", "sigma.y")
inits <- function()
list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
sigma.theta=runif(1,0,100))
parameters <- c("theta", "mu.theta", "sigma.theta")
setwd(".")
schools.sim <- bugs (data, inits, parameters,
"/usr/local/doc/r2winbugs/schools.bug",
n.chains=3, n.iter=1000, working.directory=".")
Warning message:
In file.create(to[okay]) :
cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason
'Permission denied'
--
Rodney Sparapani Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician Department of Medicine
Was 'Name That Tune' rigged? Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do Milwaukee, WI, USA
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From: Uwe L. <li...@st...> - 2008-09-12 15:08:34
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Rodney Sparapani wrote:
> Uwe Ligges wrote:
>> I cannot reproduce on Windows even when using 3 different directories:
>>
>> - one for data
>> - one as working directory
>> - one for the model file
>>
>>
>>
>> schools <- read.table ("d:/schools.dat", header=T)
>> J <- nrow (schools)
>> y <- schools$estimate
>> sigma.y <- schools$sd
>> data <- list ("J", "y", "sigma.y")
>> inits <- function()
>> list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
>> sigma.theta=runif(1,0,100))
>> parameters <- c("theta", "mu.theta", "sigma.theta")
>> setwd("d:/temp")
>> schools.sim <- bugs (data, inits, parameters, "d:/uwe/schools.bug",
>> n.chains=3, n.iter=1000, working.directory="d:/temp")
>>
>>
>> Simply works for me ....
>>
>> Uwe
> Hi Uwe:
>
> But, you have the command setwd("d:/temp") and I don't. However, this does
> not work around the problem either:
>
> library(R2WinBUGS)
> schools <- read.table ("/usr/local/doc/r2winbugs/schools.dat", header=T)
> J <- nrow (schools)
> y <- schools$estimate
> sigma.y <- schools$sd
> data <- list ("J", "y", "sigma.y")
> inits <- function()
> list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
> sigma.theta=runif(1,0,100))
> parameters <- c("theta", "mu.theta", "sigma.theta")
> setwd(".")
> schools.sim <- bugs (data, inits, parameters,
> "/usr/local/doc/r2winbugs/schools.bug",
> n.chains=3, n.iter=1000, working.directory=".")
>
>
> Warning message:
> In file.create(to[okay]) :
> cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason
> 'Permission denied'
So, what exactly is your working directory? If it is
"/usr/local/doc/r2winbugs/schools.txt", I am not surprised.
Uwe Ligges
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From: Rodney S. <rsp...@mc...> - 2008-09-12 16:21:30
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Uwe Ligges wrote:
>
>> Hi Uwe:
>>
>> But, you have the command setwd("d:/temp") and I don't. However,
>> this does
>> not work around the problem either:
>>
>> library(R2WinBUGS)
>> schools <- read.table ("/usr/local/doc/r2winbugs/schools.dat", header=T)
>> J <- nrow (schools)
>> y <- schools$estimate
>> sigma.y <- schools$sd
>> data <- list ("J", "y", "sigma.y")
>> inits <- function()
>> list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
>> sigma.theta=runif(1,0,100))
>> parameters <- c("theta", "mu.theta", "sigma.theta")
>> setwd(".")
>> schools.sim <- bugs (data, inits, parameters,
>> "/usr/local/doc/r2winbugs/schools.bug",
>> n.chains=3, n.iter=1000, working.directory=".")
>>
>>
>> Warning message:
>> In file.create(to[okay]) :
>> cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason
>> 'Permission denied'
>
>
>
> So, what exactly is your working directory? If it is
> "/usr/local/doc/r2winbugs/schools.txt", I am not surprised.
>
> Uwe Ligges
>
As I said in the original post, $HOME
--
Rodney Sparapani Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician Department of Medicine
Was 'Name That Tune' rigged? Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do Milwaukee, WI, USA
|
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From: Uwe L. <li...@st...> - 2008-09-15 16:07:20
|
Rodney Sparapani wrote:
> Uwe Ligges wrote:
>> I cannot reproduce on Windows even when using 3 different directories:
>>
>> - one for data
>> - one as working directory
>> - one for the model file
>>
>>
>>
>> schools <- read.table ("d:/schools.dat", header=T)
>> J <- nrow (schools)
>> y <- schools$estimate
>> sigma.y <- schools$sd
>> data <- list ("J", "y", "sigma.y")
>> inits <- function()
>> list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
>> sigma.theta=runif(1,0,100))
>> parameters <- c("theta", "mu.theta", "sigma.theta")
>> setwd("d:/temp")
>> schools.sim <- bugs (data, inits, parameters, "d:/uwe/schools.bug",
>> n.chains=3, n.iter=1000, working.directory="d:/temp")
>>
>>
>> Simply works for me ....
>>
>> Uwe
> Hi Uwe:
>
> But, you have the command setwd("d:/temp") and I don't. However, this does
> not work around the problem either:
>
> library(R2WinBUGS)
> schools <- read.table ("/usr/local/doc/r2winbugs/schools.dat", header=T)
> J <- nrow (schools)
> y <- schools$estimate
> sigma.y <- schools$sd
> data <- list ("J", "y", "sigma.y")
> inits <- function()
> list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
> sigma.theta=runif(1,0,100))
> parameters <- c("theta", "mu.theta", "sigma.theta")
> setwd(".")
> schools.sim <- bugs (data, inits, parameters,
> "/usr/local/doc/r2winbugs/schools.bug",
> n.chains=3, n.iter=1000, working.directory=".")
>
>
> Warning message:
> In file.create(to[okay]) :
> cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason
> 'Permission denied'
OK, I still canoot reproduce on Windows.
Can you please try to say:
options(warn=2)
# Run the example code again that produces some error now
traceback()
Can you please show us that traceback() stack?
Thank you,
Uwe
|
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From: Rodney S. <rsp...@mc...> - 2008-09-15 16:25:29
|
Uwe Ligges wrote:
> OK, I still canoot reproduce on Windows.
>
> Can you please try to say:
>
> options(warn=2)
> # Run the example code again that produces some error now
> traceback()
>
> Can you please show us that traceback() stack?
>
> Thank you,
> Uwe
>
> traceback()
10: doWithOneRestart(return(expr), restart)
9: withOneRestart(expr, restarts[[1]])
8: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
7: .signalSimpleWarning("cannot create file
'/usr/local/doc/r2winbugs/schools.txt', reason 'Permission denied'",
quote(file.create(to[okay])))
6: file.create(to[okay])
5: file.copy(model.file, new.model.file, overwrite = TRUE)
4: bugs(data, inits, parameters, "/usr/local/doc/r2winbugs/schools.bug",
n.chains = 3, n.iter = 1000, working.directory = ".")
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1: source("/usr/local/doc/r2winbugs/schools.r")
>
--
Rodney Sparapani Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician Department of Medicine
Was 'Name That Tune' rigged? Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do Milwaukee, WI, USA
|
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From: Gorjanc G. <Gre...@bf...> - 2008-09-16 06:54:10
|
Hi! Sorry for jumping in so late ... The problem seems to be the file.copy function since it tries to convert the schools.bug into schools.txt file in a folder where user does not have permission i.e. in /usr/local/doc/r2winbugs. The problematic code is on line 64 of bugs.R in the R2WinBUGS package. The WinBUGS executable only recognizes ASCII files as such if they have "txt" extension. However, a lot of us use "bug" extension to emphasize that this a BUGS model file. Therefore, the bugs() function tries to copy model_file_name.bug to model_file_name.txt. Rodney, since you are having the model_file_name.bug in a place where your user does not have permissions to write new files file copying can not be performed. I agree that this is not the behaviour we want. This issue has been raised due to two facts: stringent permissions on unix like machines and Rodneys' setup - i.e. the /usr/local/doc/r2winbugs is not writable for regular users. Perhaps, we could in such cases copy the model.file to a working directory in order to avoid this problem. This should work in any setting since the working directory must be writtable anyway. I will try to implement this so that Rodney can check. P.S. However, note the R2WinBUGS needs a write permission for the WinBUGS folder, since there is a part of the code that reads in one of the ODC files, changes something in relation with the burnin period and writes the file back. I am not familiar with the rational of this. Maybe, anyone else can enlighten me/us ... gg |
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